Abstract
We present a new efficient algorithm for exact matching in encoded DNA sequences and on binary strings. Our algorithm combines a multi-pattern version of the Bndm algorithm and a simplified version of the Commentz-Walter algorithm. We performed also experimental comparisons with the most efficient algorithms presented in the literature. Experimental results show that the newly presented algorithm outperforms existing solutions in most cases.
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Faro, S., Lecroq, T. (2009). An Efficient Matching Algorithm for Encoded DNA Sequences and Binary Strings. In: Kucherov, G., Ukkonen, E. (eds) Combinatorial Pattern Matching. CPM 2009. Lecture Notes in Computer Science, vol 5577. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02441-2_10
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DOI: https://doi.org/10.1007/978-3-642-02441-2_10
Publisher Name: Springer, Berlin, Heidelberg
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